DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant's arguments filed on January 28, 2026 have been received and entered. Claims 18, 24-26 and 27 are pending in the instant application.
Claims 18, 24-26 and 27 are pending in the instant application.
Priority
This application is a continuation of US application no 17830011 filed on June 1, 2022 which is a continuation of US application no 17/590,613 filed on 02/01/2022, now USP 11365407, which is a continuation of 17/366,290 filed on 07/02/2021 now USP 11254930, which is a continuation of 16/800,444 filed on 02/25/2020 now USP 11091756, which is a continuation of 16/601,144 filed on 10/14/2019, which claims priority from US provisional 62/864,432 filed on 06/20/2019, US provisional 62/830,654 filed on 04/08/2019, US provisional of 62/746,497 filed on 10/16/2018.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 01/28/2026 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Claims 18, 24-26 and 27 are under consideration.
Double Patenting
Claims 18, 24-26 and 27 remain provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 29-33 of copending Application No. 18/680,273 and Jaskula-Ranga et al (WO/2018/009534, EFD07/5/2016, IDS)
Although the claims at issue are not identical, they are not patentably distinct from each other because claims in both applications are directed to an isolated eukaryotic cell comprising a genome with a transgene, wherein the transgene comprises from 5' to 3' orientation: a first splice donor reverse complement, a first coding sequence reverse complement, a first promoter reverse complement, a second promoter, a second coding sequence, and a second splice donor, wherein the first coding sequence is operably linked to the first splice donor and first promoter, and the second coding sequence is operably linked to the second splice donor and second promoter.
Response to arguments
While Applicant has requested that the rejection be held in abeyance until allowable subject matter can be identified, a request of abeyance does not overcome or address an issue of obvious double patenting between claims in the instant case and application 18/680,273. Thus, the rejection is maintained.
Withdrawn -Claim Rejections - 35 USC § 103
Claims 18, 24-26 and 27 are rejected under 35 U.S.C. 103 as being unpatentable over Jaskula-Ranga et al (WO/2018/009534, EFD07/5/2016, IDS) as evidenced by Ohmori et al (Scientific Reports, 2017, 7, 4159, 1-11, IDS), Carlo et al (US20200040362, dated 02/06/2020, EFD, 06/28/2018) and Harrington et al (US6740503) as evidenced by Ni et al (PNAS, 2012, 38, 15389-15394)/ Sheng et al (Canadian Journal of Microbiology, 2014, 445-454, IDS) / Jarvis (US 2020/0231974, 7/23/2020, IDS) . Applicant’s argument that combination of cited references fails to teach or suggest a transgene wherein the first coding sequence encodes an amino acid sequence, and the second coding sequence encodes the same amino acid sequence as the first coding sequence is found persuasive, therefore, previous rejection of claims are hereby withdrawn.
Maintained -Claim Rejections - 35 USC § 112- in modified form
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 18, 24-26 and 27 remain rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph in modified form, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 18 is drawn to claims are directed an isolated genetically modified eukaryotic cell comprising a transgene integrated within an intron of an endogenous gene, wherein the transgene comprises from 5' to 3' orientation :any first splice acceptor, a first coding sequence, any first terminator, any second terminator reverse complement, a second coding sequence reverse complement, and a second splice acceptor reverse complement, wherein the first coding sequence is operably linked to the first splice acceptor and first terminator, and the second coding sequence is operably linked to the second splice acceptor and second terminator, wherein the first and second coding sequences differ in nucleic acid sequence but each encode the same amino acid sequence, wherein said amino sequences encoded by the first and second coding sequences encodes a reporter protein-- or a purification tag, wherein the transgene is equal to or less than 4.7 kb, and wherein the transgene is operably linked to the promoter of the endogenous gene.
The amended claim 18 encompasses a genus of cell comprising a transgene comprising a genus of first splice acceptor, a first coding sequence, a genus of first terminator, any second terminator reverse complement, a second coding sequence reverse complement, and any species second splice acceptor reverse complement, wherein the first coding sequence is operably linked to the first splice acceptor and first terminator, and the second coding sequence is operably linked to the second splice acceptor and second terminator integrated within any intron of any endogenous gene. The scope of the claim encompasses insertion of transgene into an intron of known or yet to be identified endogenous gene.
The specification teaches a novel transgene construct having the following structure: in a 5’ to 3’ direction, [splice acceptor 1] - [partial coding sequence 1]-[terminator 1] and a second nucleic acid having the elements [splice acceptor 2] [partial coding sequence 2] - [terminator 2] can be placed in tail-to-tail orientation resulting in [splice acceptor 1] - [partial coding sequence 1] -[terminator 1] -terminator 2 RC] - [partial coding sequence 2 RC] - [splice acceptor 2 RC], where RC refers to reverse complement.(see page 16, lines, line 18-23). The specification discloses the presence of rare-cutting endonuclease target sites flank splice acceptor sites in the transgene (see fig. 1, 6 and 7).
However, the specification does not provide adequate guidance for making any
specific, desired "integration of a transgene
within any intron of any endogenous gene " as broadly encompassed by claim 18, other than ATXN3 gene or CACNA1A gene (claim 18).
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The guidance provided in the specification is limited to a transgene that can be integrated within an intron of the endogenous gene or at an intron-exon junction of the ATXN3 gene or CACNA1A gene. The transgene can comprise a first and second partial coding sequence encoding the peptide produced by exon 10 of a non-pathogenic ATXN3 gene and can be targeted to intron 9, or the intron 9 exon 10 junction, of a pathogenic ATXN3 gene. The transgene can comprise a first and second partial coding sequence encoding the peptide produced by exon 47 of a non-pathogenic CACNA1A gene and can be targeted to intron 46, or the intron 46exon 47 junctions, of a pathogenic CACNA1A gene (see page 9, line 13-21, fig. 4, 6 see above).
The specification does not teach and does not enable to integrate a transgene within any intron of any other endogenous gene as embraced by the breadth of the claims. Further, the claims require the first and second coding sequences differ in nucleic acid sequence but encode the same amino acid sequence, wherein said amino sequence encoded by the first and second coding sequences encoding a reporter protein, a purification tag.
The amended claim encompasses a transgene that is integrated within any intron of any endogenous gene at a CRISPR/Cas9 nuclease target site, wherein the intron has a CRISPR/Cas9 target site prior to transgene integration. The instant specification as discussed above in fig. 5 and 6 explicitly discloses that the endonuclease target sites flank splice acceptor sites in the transgene for the purpose of directing integration of the transgene construct into the target genomic locus. It is emphasized that specification discloses a transgene comprising targeting sites at the 5' and 3' ends of the construct in order to direct integration into the genome and the correct functioning of the transgenes. The claims encompass a genus of first and second terminator reverse complement. The guidance provided in the specification is limited to use of bGH polyA sequence as set forth in SEQ ID NO: 5 and SV40 polyA as set forth in SEQ IDN O: 4. The art teaches terminator sequence are important in gene expression as their strength and potential for read-through transcription need to be considered. Ren (Synthetic and Systems Biotechnology 10 (2025) 326–335) teaches terminator characteristics contributed to the upstream mRNA stability and changing the composition of bases downstream of the terminator impact the efficiency of the terminator (see page 327, col. 1, para. 1-2). Ren discloses that terminators with varied strength affect upstream mRNA stability (see page 329, col. 1, para. 2). The art further teaches that transgene inserted within an intron of an endogenous gene could interfere with function of the endogenous gene by disrupting the RNA splicing. Sironen et al (PNAS, 2006, 103, 5006-5011) studied the sequence analysis of a candidate gene KPL2 that showed the presence of an inserted retrotransposon within an intron. The insertion affected the splicing of the KPL2 transcript in two ways; it either causes skipping of the upstream exon, or causes the inclusion of an intronic sequence as well as part of the insertion in the transcript. Both changes alter the reading frame leading to premature termination of translation (abstract). In view of foregoing, it is apparent that insertion of transgene can introduce new splicing patterns, leading to the production of different mRNA isoforms that might have altered functions. The specification fails to disclose integrating a transgene comprising a first coding sequence, genus of first terminator, any second terminator reverse complement, a second coding sequence reverse complement within any intron of any endogenous locus other than a transgene can also comprise a first and second partial coding sequence and bGH polyA sequence as set forth in SEQ ID NO: 5 and SV40 polyA as set forth in SEQ IDN O: 4 that can be targeted into intron 9, or the intron 9 exon 10 junction, of a pathogenic ATXN3 gene or into intron 46, or the intron 46exon 47 junctions, of a pathogenic CACNA1A gene (see page 9, line 13-21, fig. 4, 6 see above). The specification lacks written description for "an isolated eukaryotic cell" comprising a transgene comprising a first splice acceptor, a first coding sequence, a genus of first terminator, any second terminator reverse complement, a second coding sequence reverse complement, and a second splice acceptor reverse complement integrated within any intron of any endogenous gene as broadly claimed for the reasons discussed above.
The claimed invention as a whole is not adequately described if the claims require essential or critical elements which are not adequately described in the specification and which is not conventional in the art as of applicants effective filing date. Possession may be shown by actual reduction to practice, clear depiction of the invention in a detailed drawing or by describing the invention with sufficient relevant identifying characteristics such that a person skilled in the art would recognize that the inventor had possession of the claimed invention. Pfaff v. Wells Electronics. Inc., 48 USPQ2d 1641, 1646 (1998).
In the instant case, the claimed embodiments of eukaryotic cell comprising a transgene integrated within any intron or any endogenous gene, other than those exemplified for a transgene can also comprise a first and second partial coding sequence and bGH polyA sequence as set forth in SEQ ID NO: 5 and SV40 polyA as set forth in SEQ IDN O: 4 that can be targeted into intron 9, or the intron 9 exon 10 junction, of a pathogenic ATXN3 gene or into intron 46, or the intron 46exon 47 junctions, of a pathogenic CACNA1A gene encompassed within the genus of transgene combination sequences lack a written description. The specification fails to describe what DNA molecules fall into this genus of endogenous gene to be integrated within plurality of intron of a genus of endogenous gene. The skilled artisan cannot envision the detailed chemical structure of the encompassed by the transgene to be integrated into an endogenous gene, and therefore conception is not achieved until reduction to practice has occurred, regardless of the complexity or simplicity of the method of isolation. Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method of isolating it. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (Fed. Cir. 1993) and Amgen lnc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016 (Fed. Cir. 1991).
In view of the above considerations one of skill in the art would not recognize that applicant was in possession of the necessary common features or attributes possessed by member of the genus of transgene to be integrated within any intron of any endogenous gene, other than those exemplified for ATXN3 gene or CACNA1A.
Response to arguments
Applicant disagree with the rejection arguing that information that is available to the skilled artisan does not need to, and should not, be copied into the specification for it could unreasonably increase the size of a patent specification unnecessarily. See MPEP 2163. Here, the earliest filed provisional teaches, inter alia, that "In one embodiment, this document features methods for modifying the 3' end of endogenous genes, where endogenous genes have at least one intron between two coding exons. The intron can be any intron which is removed from precursor messenger RNA by normal messenger RNA processing machinery. The intron can be between 20 bp and >500 kb and comprise elements including a splice donor site, branch sequence, and acceptor site. Applicant argues that there were numerous studies in the literature describing the existence of canonical sequences and structures in eukaryotic organisms, which one of ordinary skill in the art would have been aware of and would have been able to recognize in an endogenous gene. See, for example, Will, C.L. et al., Cold Spring Harb Perspect Biol 2011. This is similar with terminators, such as eukaryotic terminators, including SV40 and bGH, comprise consensus RNA processing and polyadenylation sequences for directing termination. See, for example, Connelly et al (Genes Dev. 1988 Apr;2(4):440-52). Furthermore, the specification provides evidence that the transgene of the claimed cell integrates into introns of at least two genes, confirming effectiveness of the transgenes and methods.
Applicant notes that the claimed cell only needs to carry a reporter protein or a purification tag. There is no requirement that the cell function in the same way as the wildtype cell, i.e., a cell not modified by the claimed transgene. Consequently, it is irrelevant whether the insertion of the claimed transgene changes the splicing of the endogenous gene to create new isoforms or causes any other functional changes to the cell. So long as the cell expresses the reporter gene (which can easily be determined because by definition the reporter will report which cells have been modified and the tag can be equally easily detected), the cell falls within the scope of the claims. Scientists are equipped to routinely assess whether reporter/tag integration resulted in any functional changes to the cell or not. They can sequence the modified endogenous gene to confirm proper integration; they can determine whether new isoforms are being expressed; and they can do all manner of functional studies to evaluate if the reporter/tag insertion functionally modified the cell. But all that is irrelevant to the claimed method and resulting cell. So long as the cell has been modified by a transgene as claimed and, as a result, encodes the claimed reporter or tag, the cell is within the scope of the claims.
In response as stated in previous office action, the issue pertains to a genus of isolated eukaryotic cells that encompass a genus of all animals, plants, and fungi cells comprising a transgene integrated within an intron of an endogenous gene.
The specification explicitly teaches transgene comprises first and second splice acceptor sequence, a first and second “partial coding sequence”, and a first and second terminator (see page 2, lines 28-30, page 5, lines 8-9 and page 7 lines 18-20). Examiner in part agrees with the applicant’s argument that instant specification teaches a method for modifying the 3' end of endogenous genes, where endogenous genes have at least one intron between two coding exons. The intron can be any intron which is removed from precursor messenger RNA by normal messenger RNA processing machinery. The intron can be between 20 bp and >500 kb and comprise elements including a splice donor site, branch sequence, and acceptor site. This is further exemplified wherein the transgene could be integrated within an intron of the endogenous gene at an intron-exon junction of the partial ATXN3 gene or partial CACNA1A gene in a HEK293T (human or mammalian) cells (see examples 1-4). The exemplified transgenes disclosed in specification all contain a partial coding sequence. The term "partial coding sequence" is defined as a sequence of nucleic acids that encodes a partial protein. The partial coding sequence can encode a protein that comprises one or less amino acids as compared to the wild type protein or functional protein (see page 17, line 8-12). In view of foregoing, it is apparent that a partial coding sequence exampled in the specification is different from a coding sequence as claimed in the instant application. The specification prophetically discloses transgenes for the modification of the 3' end of endogenous genes can comprise multiple functional elements, including target sites for rare-cutting endonucleases, homology arms, splice acceptor sequences, coding sequences, and transcription terminators (FIG. 1). There is no disclosure of a transgene that contains only splice acceptor sequences, coding sequences, and transcription terminators (e.g., SA1-CDS1-T1-T2- CDS2-SA2).
In response to applicant’s argument in part relying on Will and Connelly it is emphasized that the issue is not whether canonical sequences and structures in eukaryotic organisms and eukaryotic terminators are well known in prior art. The issue pertains to prior art reporting insertion of transgene within an intron of different genes (eukaryotic gene) may affect the splicing of the endogenous gene transcript either causing skipping of the upstream exon, or triggering the inclusion of an intronic sequence as well as part of the insertion in the transcript. It is emphasized that both changes alter the reading frame leading to premature termination of translation. This is supported by Sironen et al (PNAS, 2006, 103, 5006-5011) who studied the sequence analysis of a candidate gene KPL2 that showed the presence of an inserted retrotransposon within an intron. The insertion affected the splicing of the KPL2 transcript in two ways; it either causes skipping of the upstream exon, or causes the inclusion of an intronic sequence as well as part of the insertion in the transcript. Both changes alter the reading frame leading to premature termination of translation (abstract). It is further disclosed that alternative splicing, which can generate a range of protein isoforms by the inclusion or skipping of exons, often in a cell-type or developmental stage-specific manner (see page 5009, col. 2, para. 2). These assertions are further supported in another publication that shows inserting gene trap cassette into intron activates cryptic splice sites thereby generating abnormal transcripts suggesting intronic insertions could be unpredictably later RNA splicing instead a simple insertion (see Osipovich et al Nucleic Acids Res . 2004 May 20;32(9):2912–2924, cited as evidence without relying on the rejection).
Applicant’s argument that it is irrelevant whether the insertion of the claimed transgene changes the splicing of the endogenous gene to create new isoforms or causes any other functional changes to the cell as long as the cell expresses the reporter gene is not found persuasive. It should be noted that abnormal splicing of endogenous gene (i) could retain part of the intron or cause a frameshift in the endogenous exons resulting in inserted tag/reporter to be out of the frame; or (ii) is translated resulting protein that is likely to be unstable or non-functional chimeric protein. Further, the tag/reporter sequence inserted within the intron of an endogenous gene’s transcript would result on the host gene’s splicing machinery to correctly process the mRNA. If an insertion results in an aberrant splice-site, it would alter both the endogenous gene function and resulting expression of tag/reporter sequence. In view of foregoing, it is apparent that the insertion site to restore native splice-donor and splice-acceptor sequences is critical for the resulting expression of tag/reporter gene. In the case, claims as such do not require expression of tag/reporter gene. Further, the specification fails to provide adequate number of representative species by describing the invention with sufficient relevant identifying characteristics such that a person skilled in the art would recognize that the inventor had possession of the inserting a tag/reporter gene within any intron of any known endogenous or yet to be identified endogenous gene other than inserting the transgene comprising a first and second partial coding sequence and bGH polyA sequence as set forth in SEQ ID NO: 5 or SV40 polyA as set forth in SEQ IDN O: 4 that can be targeted into intron 9, or the intron 9 exon 10 junction, of a pathogenic ATXN3 gene or into intron 46, or the intron 46exon 47 junctions, of a pathogenic CACNA1A gene. In view of the above considerations one of skill in the art would not recognize that applicant was in possession of the necessary common features or attributes possessed by member of the genus of transgene to be integrated within any intron of any endogenous gene, other than those exemplified for ATXN3 gene or CACNA1A.
Conclusion
No claims allowed.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Finn (US 20200270617, EFD 10/18/2018) and INTELLIA THERAPEUTICS, ("Q3 2018 Earnings and Corporate Development", Power point, 23 pages, presented 31 Oct 2018, IDS) teaches a nucleic acid construct is a bidirectional nucleic acid construct. In some embodiments, the construct comprises: i. a first segment comprising a coding sequence for a heterologous polypeptide; and ii. a second segment comprising a reverse complement of a coding sequence of the heterologous polypeptide. In some embodiments, the construct comprises a polyadenylation signal sequence. In some embodiments, the construct comprises a splice acceptor site. In some embodiments, the construct does not comprise a homology arm (see para. 12, Fig. 1-5). Finn is not applied as prior art as effective filing date of Finn is 2 days after the EFD of instant application.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ANOOP K. SINGH whose telephone number is (571)272-3306. The examiner can normally be reached Monday-Friday, 8AM-5PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Peter Paras can be reached at (571)272-4517. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/ANOOP K SINGH/ Primary Examiner, Art Unit 1632
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